Identification of functional genomic regions with copy number alteration in liver cancer

Tzu Hung Hsiao, Hung I.Harry Chen, Yidong Chen

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Abstract

Copy number alterations (CNAs) happen frequently in solid tumors. Several oncogenes and tumor suppressor genes have been identified with CNAs. However, the systematic survey of CNA regulated functions is still lack. By employing systems biology approaches, instead of examining individual genes, we directly identified the spatial functional hotspots in human genome. Total 249 genomic regions, or segments, with 410 enriched biological functions were identified. An aCGH data set of hepatocellular carcinoma (HCC) tumors was employed in this study and several putative affected functions of CNAs were identified. Our results indicate that 4 immune related segments were lost in most of patients. In addition, our data implied these immune related segments might be involved in HCC oncogenesis. The result further demonstrated that our method enables researchers to survey biological functions of CNAs and to construct regulation hypothesis at pathway and functional levels.

Original languageEnglish (US)
Title of host publicationProceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2012
Pages155-158
Number of pages4
DOIs
StatePublished - Dec 1 2012
Event2012 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2012 - Washington, DC, United States
Duration: Dec 2 2012Dec 4 2012

Publication series

NameProceedings - IEEE International Workshop on Genomic Signal Processing and Statistics
ISSN (Print)2150-3001
ISSN (Electronic)2150-301X

Other

Other2012 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2012
Country/TerritoryUnited States
CityWashington, DC
Period12/2/1212/4/12

Keywords

  • Copy number alteration
  • gene set enrichment
  • liver cancer
  • pathway analysis

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology (miscellaneous)
  • Computational Theory and Mathematics
  • Signal Processing
  • Biomedical Engineering

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